Polymer–metal complexes of polydimethylsiloxanes are especially promising materials because of their self–healing ability. The structural models of the copolymer of,–(3–aminopropyl)polydimethylsiloxane and 2,6–pyridinedicarboxamide coordinating Ni(II) ions in various proportions were constructed using the molecular dynamics simulation methods and fragment condensation approach. The glass transition temperature, isothermal compressibility coefficient, and volumetric coefficient of thermal expansion were estimated. For the developed structural models those characteristics did not have an apparent dependence on the Ni(II) content. The analysis of structural organization of copolymeric models revealed that the water molecules were aggregated in clusters in proximity to the Ni(II) 2,6–pyridinedicarboxamide homoleptic complexes. The geometrical characteristics of the copolymer chains coiled into irregular helices were determined. The methodology of the chain twisting estimation was proposed.